For genomic regions where there were multiple genes showing significant SMR associations, we attempted to resolve these with conditional analysis using GCTA-COJO42,43. We selected the top-associated cis-eQTL for one gene (or a set of genes sharing the same cis-eQTL) ran a COJO analysis in the schizophrenia GWAS data and the eQTL data for each of the other genes conditioning on the selected top cis-eQTL. We then re-ran the SMR and HEIDI analyses using these conditional GWAS and eQTL results.
